AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene056595


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene056595.t1 MTR_4g068100 96.296 81 3 0 1 81 173 253 9.38e-53 164
MS.gene056595.t1 MTR_4g068100 96.296 81 3 0 1 81 235 315 3.97e-52 165
MS.gene056595.t1 MTR_4g068100 96.296 81 3 0 1 81 243 323 4.41e-52 165
MS.gene056595.t1 MTR_2g099090 71.605 81 23 0 1 81 233 313 7.71e-38 128
MS.gene056595.t1 MTR_2g099090 71.605 81 23 0 1 81 249 329 8.84e-38 128
MS.gene056595.t1 MTR_4g068100 97.059 34 1 0 1 34 235 268 7.45e-17 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene056595.t1 AT1G06130 71.250 80 23 0 2 81 250 329 4.58e-36 124
MS.gene056595.t1 AT1G06130 71.250 80 23 0 2 81 249 328 4.63e-36 124
MS.gene056595.t1 AT2G31350 67.500 80 26 0 2 81 245 324 5.61e-35 121
MS.gene056595.t1 AT2G31350 67.500 80 26 0 2 81 244 323 5.62e-35 121
MS.gene056595.t1 AT2G43430 58.750 80 33 0 2 81 207 286 3.45e-28 102
MS.gene056595.t1 AT2G43430 58.750 80 33 0 2 81 234 313 5.25e-28 102
MS.gene056595.t1 AT2G43430 58.750 80 33 0 2 81 252 331 6.31e-28 102

Find 19 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGGCAAGCCTTTATTTCTA+AGG 0.334734 4.3:+36893507 None:intergenic
GTAGCTCACCTTAGAAATAA+AGG 0.360851 4.3:-36893515 MS.gene056595:CDS
AGCAGATGACGCTGAAGCCC+TGG 0.379819 4.3:-36892987 MS.gene056595:CDS
TCGCCGGATTTCCGTGCTCC+AGG 0.437127 4.3:+36893030 None:intergenic
GTGCTCCAGGTGCGAAGGAA+TGG 0.447198 4.3:+36893043 None:intergenic
GCACCTGGAGCACGGAAATC+CGG 0.447279 4.3:-36893033 MS.gene056595:CDS
GCAATCCATTCCTTCGCACC+TGG 0.451189 4.3:-36893048 MS.gene056595:CDS
CTGCTTGTCGAATGACACCC+AGG 0.508543 4.3:+36892969 None:intergenic
GGTTCCAACTACACTGAAGA+TGG 0.510396 4.3:-36893080 MS.gene056595:CDS
AACTACACTGAAGATGGAAA+AGG 0.523886 4.3:-36893074 MS.gene056595:CDS
GGCTTCAGCGTCATCTGCTG+TGG 0.537522 4.3:+36892991 None:intergenic
GCAGATGACGCTGAAGCCCT+GGG 0.542024 4.3:-36892986 MS.gene056595:CDS
GTGAGCTACATGTGAAGCAT+AGG 0.556012 4.3:+36893529 None:intergenic
ATTCCTTCGCACCTGGAGCA+CGG 0.576893 4.3:-36893041 MS.gene056595:CDS
TTTCCGTGCTCCAGGTGCGA+AGG 0.583123 4.3:+36893038 None:intergenic
GTCCATAGATCCTCAAAACA+AGG 0.614843 4.3:-36893561 MS.gene056595:CDS
TAGAAATAAAGGCTTGCCCA+CGG 0.627749 4.3:-36893504 MS.gene056595:intron
TGCTTGTCGAATGACACCCA+GGG 0.629657 4.3:+36892970 None:intergenic
GGGTGTCATTCGACAAGCAG+AGG 0.637765 4.3:-36892966 MS.gene056595:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAAATGATTTCTGAAATAT+TGG + chr4.3:36893123-36893142 None:intergenic 15.0%
!! AATCTAAATCCATTGGTTAT+TGG - chr4.3:36893376-36893395 MS.gene056595:intron 25.0%
!! ACTTCGTAAATTTTTACTGA+AGG + chr4.3:36893195-36893214 None:intergenic 25.0%
!! CTTCGTAAATTTTTACTGAA+GGG + chr4.3:36893194-36893213 None:intergenic 25.0%
!!! ATACATGTTAGTTTTTGATC+GGG - chr4.3:36893165-36893184 MS.gene056595:intron 25.0%
!!! CATACATGTTAGTTTTTGAT+CGG - chr4.3:36893164-36893183 MS.gene056595:intron 25.0%
ACAAATTATTCATGTTTCCC+AGG - chr4.3:36893435-36893454 MS.gene056595:intron 30.0%
TCAAACATACCAATAACCAA+TGG + chr4.3:36893388-36893407 None:intergenic 30.0%
TTTGTTAAAAGCAGAATGCA+GGG + chr4.3:36893420-36893439 None:intergenic 30.0%
! AACTTCGCTTCTTTTACAAA+TGG - chr4.3:36893065-36893084 MS.gene056595:CDS 30.0%
! ACAAGCAGAGGATAATTTTT+AGG - chr4.3:36893582-36893601 MS.gene056595:CDS 30.0%
! ATTTGTTAAAAGCAGAATGC+AGG + chr4.3:36893421-36893440 None:intergenic 30.0%
AACTACACTGAAGATGGAAA+AGG - chr4.3:36893462-36893481 MS.gene056595:intron 35.0%
GTAGCTCACCTTAGAAATAA+AGG - chr4.3:36893021-36893040 MS.gene056595:CDS 35.0%
! TATGTGGTTCTTTTAGTGCA+GGG - chr4.3:36893353-36893372 MS.gene056595:intron 35.0%
! TTTTCCATCTTCAGTGTAGT+TGG + chr4.3:36893463-36893482 None:intergenic 35.0%
!!! GATTGAAGTTCCTTGTTTTG+AGG + chr4.3:36892988-36893007 None:intergenic 35.0%
!!! TTCCTTGTTTTGAGGATCTA+TGG + chr4.3:36892980-36892999 None:intergenic 35.0%
AAGAACCACATAGTTGCTAC+AGG + chr4.3:36893345-36893364 None:intergenic 40.0%
GAAGTTTGCAAACTTACCGT+GGG + chr4.3:36893051-36893070 None:intergenic 40.0%
GTCCATAGATCCTCAAAACA+AGG - chr4.3:36892975-36892994 MS.gene056595:CDS 40.0%
TAGAAATAAAGGCTTGCCCA+CGG - chr4.3:36893032-36893051 MS.gene056595:CDS 40.0%
TGCAGGGAATCTAAATCCAT+TGG - chr4.3:36893369-36893388 MS.gene056595:intron 40.0%
! CTATGTGGTTCTTTTAGTGC+AGG - chr4.3:36893352-36893371 MS.gene056595:intron 40.0%
!! TGGGCAAGCCTTTATTTCTA+AGG + chr4.3:36893032-36893051 None:intergenic 40.0%
!!! CTGCAACTTTTAGTTTTCGC+CGG + chr4.3:36893525-36893544 None:intergenic 40.0%
AGTTGCCTGTAGCAACTATG+TGG - chr4.3:36893337-36893356 MS.gene056595:intron 45.0%
CAGGCAACTAGGCAAGAAAT+CGG + chr4.3:36893326-36893345 None:intergenic 45.0%
CATAGTTGCTACAGGCAACT+AGG + chr4.3:36893337-36893356 None:intergenic 45.0%
CGAAGTTTGCAAACTTACCG+TGG + chr4.3:36893052-36893071 None:intergenic 45.0%
CTTCAGTGTAGTTGGAACCT+GGG + chr4.3:36893455-36893474 None:intergenic 45.0%
GAAGTCACTGCAGTTACTGT+TGG - chr4.3:36893210-36893229 MS.gene056595:intron 45.0%
GGTTCCAACTACACTGAAGA+TGG - chr4.3:36893456-36893475 MS.gene056595:intron 45.0%
GTGAGCTACATGTGAAGCAT+AGG + chr4.3:36893010-36893029 None:intergenic 45.0%
TCTTCAGTGTAGTTGGAACC+TGG + chr4.3:36893456-36893475 None:intergenic 45.0%
TGCTTGTCGAATGACACCCA+GGG + chr4.3:36893569-36893588 None:intergenic 50.0%
ATTCCTTCGCACCTGGAGCA+CGG - chr4.3:36893495-36893514 MS.gene056595:intron 55.0%
CTGCTTGTCGAATGACACCC+AGG + chr4.3:36893570-36893589 None:intergenic 55.0%
GCAATCCATTCCTTCGCACC+TGG - chr4.3:36893488-36893507 MS.gene056595:intron 55.0%
!! GGGTGTCATTCGACAAGCAG+AGG - chr4.3:36893570-36893589 MS.gene056595:CDS 55.0%
AGCAGATGACGCTGAAGCCC+TGG - chr4.3:36893549-36893568 MS.gene056595:CDS 60.0%
GCACCTGGAGCACGGAAATC+CGG - chr4.3:36893503-36893522 MS.gene056595:intron 60.0%
GCAGATGACGCTGAAGCCCT+GGG - chr4.3:36893550-36893569 MS.gene056595:CDS 60.0%
GGCTTCAGCGTCATCTGCTG+TGG + chr4.3:36893548-36893567 None:intergenic 60.0%
GTGCTCCAGGTGCGAAGGAA+TGG + chr4.3:36893496-36893515 None:intergenic 60.0%
TTTCCGTGCTCCAGGTGCGA+AGG + chr4.3:36893501-36893520 None:intergenic 60.0%
TCGCCGGATTTCCGTGCTCC+AGG + chr4.3:36893509-36893528 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 36892955 36893603 36892955 ID=MS.gene056595
chr4.3 mRNA 36892955 36893603 36892955 ID=MS.gene056595.t1;Parent=MS.gene056595
chr4.3 exon 36893505 36893603 36893505 ID=MS.gene056595.t1.exon1;Parent=MS.gene056595.t1
chr4.3 CDS 36893505 36893603 36893505 ID=cds.MS.gene056595.t1;Parent=MS.gene056595.t1
chr4.3 exon 36892955 36893101 36892955 ID=MS.gene056595.t1.exon2;Parent=MS.gene056595.t1
chr4.3 CDS 36892955 36893101 36892955 ID=cds.MS.gene056595.t1;Parent=MS.gene056595.t1
Gene Sequence

>MS.gene056595

GATAATTCAAAGTTTGCATTGTCCATAGATCCTCAAAACAAGGAACTTCAATCCTATGCTTCACATGTAGCTCACCTTAGAAATAAAGGCTTGCCCACGGTAAGTTTGCAAACTTCGCTTCTTTTACAAATGGTTTGAAATACTCTCTTCTCTAACTGCTCATTACCAATATTTCAGAAATCATTTTTATTAAACTTTTATTAAGCTTACATACATGTTAGTTTTTGATCGGGATTCCCTTCAGTAAAAATTTACGAAGTCACTGCAGTTACTGTTGGATTAAGATCAGACAACTCACGTTTCAACTTTGATGCATTCAGTTCAAAAATACAAACTTGAAACGTGAGCTGCTCGTTCTAGATTCTAATCCGATTTCTTGCCTAGTTGCCTGTAGCAACTATGTGGTTCTTTTAGTGCAGGGAATCTAAATCCATTGGTTATTGGTATGTTTGAAATTGAATACCCTGCATTCTGCTTTTAACAAATTATTCATGTTTCCCAGGTTCCAACTACACTGAAGATGGAAAAGGCTTGCAATCCATTCCTTCGCACCTGGAGCACGGAAATCCGGCGAAAACTAAAAGTTGCAGCCACAGCAGATGACGCTGAAGCCCTGGGTGTCATTCGACAAGCAGAGGATAATTTTTAG

Protein sequence

>MS.gene056595.t1

DNSKFALSIDPQNKELQSYASHVAHLRNKGLPTVPTTLKMEKACNPFLRTWSTEIRRKLKVAATADDAEALGVIRQAEDNF